☰ Navigation Tabs
Crystal structure of Zika Virus NS2B-NS3 protease in complex with compound 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LC0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.75 293.15 12.00 %w/v PEG 8K
20.00 %v/v Glycerol
0.16 M Mg Acet
0.08 M Na Cacod
Crystal Properties Matthews coefficient Solvent content 2.62 53.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.793 α = 90 b = 57.472 β = 96.406 c = 72.447 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293.15 PIXEL DECTRIS EIGER2 X 9M 2025-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.88560 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.291 44.961 89.6 0.141 0.995 6.8 6.6 14363
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.291 2.581 1.53 0.508
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.291 44.956 14363 733 62.617 0.191 0.189 0.1947 0.2357 0.2382 48.785
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.091 -0.593 0.386 -0.335
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_6_deg 18.356 r_dihedral_angle_2_deg 14.173 r_dihedral_angle_3_deg 12.328 r_dihedral_angle_6_deg 12.19 r_lrange_it 7.452 r_lrange_other 7.445 r_dihedral_angle_1_deg 7.022 r_mcangle_it 5.041 r_mcangle_other 5.04 r_scangle_it 4.806
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_6_deg 18.356 r_dihedral_angle_2_deg 14.173 r_dihedral_angle_3_deg 12.328 r_dihedral_angle_6_deg 12.19 r_lrange_it 7.452 r_lrange_other 7.445 r_dihedral_angle_1_deg 7.022 r_mcangle_it 5.041 r_mcangle_other 5.04 r_scangle_it 4.806 r_scangle_other 4.804 r_mcbond_other 2.953 r_mcbond_it 2.952 r_scbond_it 2.891 r_scbond_other 2.89 r_angle_refined_deg 1.282 r_angle_other_deg 0.513 r_symmetry_nbd_other 0.174 r_nbd_refined 0.171 r_nbtor_refined 0.168 r_nbd_other 0.153 r_xyhbond_nbd_refined 0.148 r_symmetry_nbd_refined 0.102 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.066 r_ncsr_local_group_1 0.034 r_ext_dist_refined_b 0.015 r_symmetry_xyhbond_nbd_other 0.007 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2462 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction XSCALE data scaling PHENIX phasing